okay ... here's my theory
Wiess isnt back for a third season if he went after "sloane" not irina like someone else said and weiss got shot, maybe that is one thing.
The whole "dream or reality sequence" this is my take - there is no way she is married to vaughan as he said "you've been gone so long, we had to move on, we thought you were dead, you've been missing" so that means that someone would have had to remove her body from the scene right after it happened ... sark possibly? They didn't give too much away in the sense of trying to put together what happened if it was a reality. My gut feeling is that it IS a dream and this is what "could" have happened, only because of the last 5 mins, i could be wrong, but JJ has simplified the show since the super bowl episode ( ALOT SIMPLER) and it has become more "mainstream" in order to attrach a larger viewer base.
I think they will stick with this dream sequeence for a few episodes maybe look at what would have happened when she was gone, how everyone moved on, what sloane and her mother did and then syd will wake up from her coma and realize it was a dream.
Remember what her mother said. "You are the one in the prophecy, not me" that I think is foreshadowing the sloane showdown. Her mother is trying to help her as she has realized that only sydney can stop sloane. Syd can;t be gone for 2 years without sloane using the rambaldi device so that would screw up the storyline of the prophecy if she was "out of commission" for two years? doesn't that make sense? They were finally moving back towards the rambaldi device, it wouldn't make sense to jump the story line at this point ... it was so close.